title: Colon epithelium, Stat3flfl VilCre-, biolrep2

value: Stat3floxflox VillinCre-


title: adipose brown 29

status: Public on May 08 2009

type: RNA

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

country: USA

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures using GCS3000 scanner

data_processing: RMA

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: 2 ug total RNA was used with the GeneChip WT Sense Target Labeling Kit

extract_protocol: Total RNA was isolated from cell pellets using Trizol (Invitrogen, Carlsbad, CA) followed by clean up using the RNeasy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: RNA extraction from tissues of naïve male (except females for specific organs) C57BL/6J mice, 8-10 weeks of age

tag: tissue

value: adipose brown


title: F3-treated THP-1 cells for 6 hrs, biological rep1

city: Taipei

first: Hsueh-Fen

last: Juan

address: No. 1, Sec. 4, Roosevelt Road

department: Institute of Molecular and Cellular Biology

country: Taiwan

institute: National Taiwan University

description: established from the peripheral blood of a 1-year-old boy with acute monocytic leukemia (AML) at relapse in 1978; the cells can be used for induction of differentiation studies

hyb_protocol: see the Affymetrix website

scan_protocol: see the Affymetrix website

data_processing: Affymetrix Microarray Suite v5.0 software

organism: Homo sapiens

source_name: human acute monocytic leukemia

label_protocol: see the Affymetrix website

growth_protocol: The human acute monocytic leukemia THP-1, and was grown in RPMI 1640 medium supplemented with 10% fetal calf serum (Gibco BRL, Eggenstein, Germany)

extract_protocol: RNA Midi Kit from Qiagen

treatment_protocol: Cells were treated with F3 at a final concentration of 30 ug/mL for 6 or 24 hours. Controlled samples of un-induced cells were treated in the same way with the same amount of medium.

tag: cell line


title: lymph nodes 12

value: lymph nodes


title: ovary 14

description: ovary

source_name: ovary

value: ovary


title: Colon epithelium, Stat3flfl VilCre+, biolrep1

city: Erlangen

first: Clemens

last: Neufert

address: Ulmenweg 18

department: First Department of Medicine

country: Germany

description: Gene expression data from  acute DSS colitis

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array 430 2.0 in Affymetrix GeneChip Hybridization oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Arrayassist version 5.5.1 (Stratagene) using GC-RMA as normalization method, followed by log scale transformation, grouping (cre- vs cre+), baseline transformation and advanced significance analysis including unpaired t-test.

source_name: colon epithelium, DSS colitis (2.5%), d5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals were kept under SPF condition, Colitis was induced by dextran sodium sulphate (2.5 %) in the drinking water for 5 days

extract_protocol: Total RNA was purified by RNeasy Microkit as recommended by the manufacturer (Qiagen) including on column DNA digestion as recommended by the manufacturer (Qiagen)

value: Colon epithelium

tag: genotype

value: Stat3floxflox VillinCre+


title: Paracoccidioides brasiliensis_mycelia_5 days in culture_flask1_rep1

type: mixed

city: San Jose

first: Jomar

middle: Patrício

last: Monteiro

address: 2260 Clove Drive

department: Division of Infectious Diseases and Geographic Medicine

institute: Stanford University

description:
Cited Bibliography:
Clemons, K. V., Feldman, D. & Stevens, D. A. (1989). Influence of oestradiol on protein expression and methionine utilization during morphogenesis of Paracoccidioides brasiliensis. J Gen Microbiol 135, 1607-1617.
Gadgil, M., Lian, W., Gadgil, C., Kapur, V. & Hu, W. S. (2005). An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays. BMC Genomics 6, 66.
Li, X., Gu, W., Mohan, S. & Baylink, D. J. (2002). DNA microarrays: their use and misuse. Microcirculation 9, 13-22.
McCullough, M. J., DiSalvo, A. F., Clemons, K. V., Park, P. & Stevens, D. A. (2000). Molecular epidemiology of Blastomyces dermatitidis. Clin Infect Dis 30, 328-335.
Oefner, P. J., Hunicke-Smith, S. P., Chiang, L., Dietrich, F., Mulligan, J. & Davis, R. W. (1996). Efficient random subcloning of DNA sheared in a recirculating point-sink flow system. Nucleic Acids Res 24, 3879-3886.
Restrepo, A. & Jimenez, B. E. (1980). Growth of Paracoccidioides brasiliensis yeast phase in a chemically defined culture medium. J Clin Microbiol 12, 279-281.
Stover, E. P., Schar, G., Clemons, K. V., Stevens, D. A. & Feldman, D. (1986). Estradiol-binding proteins from mycelial and yeast-form cultures of Paracoccidioides brasiliensis. Infect Immun 51, 199-203.
Talaat, A. M., Howard, S. T., Hale, W. t., Lyons, R., Garner, H. & Johnston, S. A. (2002). Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. Nucleic Acids Res 30, e104.
Thorstenson, Y. R., Hunicke-Smith, S. P., Oefner, P. J. & Davis, R. W. (1998). An automated hydrodynamic process for controlled, unbiased DNA shearing. Genome Res 8, 848-855.
Williams, B. A., Gwirtz, R. M. & Wold, B. J. (2006). Genomic DNA as a general cohybridization standard for ratiometric microarrays. Methods Enzymol 410, 237-279.

hyb_protocol: PREHYBRIDIZATION Microarray slides were prepared for hybridization as follows: spotted DNA was cross-linked to the slide under a UV light source (150-300 mjoules on a UV Stratalinker® 1800; Stratagene).  Slides were incubated in 500 ml prehybridization solution (3x SSC containing 0.1 % SDS and 0.1 mg/ml bovine serum albumin (Sigma-Aldrich)) for 90 minutes at 50 C in a water bath (Li et al., 2002).  Slides were washed sequentially with water at ~100 C for 1-2 minutes, water for at room temperature 1-2 minutes and dipped five times in ethanol.  The slides were placed in 50 ml polypropylene centrifuge tubes (Corning) and centrifuged for 5 minutes at 500 x g or until dry.  Slides were stored in clean, tightly sealed containers. HYBRIDIZATION Samples of labeled nucleic acids for hybridization were concentrated using a Microcon® YM-30 Centrifugal Filter Device (Millipore) and suspended to 40 μl with 3X saline-sodium citrate buffer (Sigma-Aldrich, St. Louis, MO), 0.1% sodium dodecyl sulfate (Sigma-Aldrich). These samples were incubated at 100oC for 2 minutes, 37 C for 15-25 minutes, transferred onto a microarray slide and covered with a coverslip and placed in hybridization chambers (see supplemental material for details).  Hybridization was carried at 50 C for 14 to 18 hours followed by washing the slides with 2X SSC with 0.03% SDS, 2X SSC, 1X SSC and 0.2X SSC for 2-5 minutes in each solution (500 ml volume/solution) and spin drying. Slides were scanned within 24 hours (GenePix® 4000B Microarray Scanner, Axon Instruments, Union City, CA).  All hybridization experiments were done in duplicate from each of two independent cultures.

scan_protocol: Hybridized microarrays were scanned in a GenePix® 4000B Microarray Scanner (Axon Instruments, Union City, CA). Raw data were extracted by GenePix® Pro 6.0 Microarray Image Analysis software (Axon) and analyzed using Array-A-Lizer (Petri et al., 2004) for slide quality control estimations (background intensity and spot intensity distribution).  Scanner photomultiplier tube gains for both detection channels, 635 nm (Cy5-red color) and 532 nm (Cy3-green color), were 540 and 500, respectively.

data_processing: Gene expression data underwent global normalization using the R statistical package to perform quantile normalization of the global reference channel by computing the centroid of all global reference signatures, and performing a loess fit of each individual global reference signature to the centroid.  The loess curve for a given sample was then used to scale both channels for each gene in that sample.  Data was further normalized in GeneSpring GX 7.3.1 (Agilent Technologies, Palo Alto, CA) as follows: per spot to the gDNA channel, and per gene to each gene’s respective median (Talaat et al., 2002).  For M versus Y gene expression, per slide normalization consisted of selecting a list of spots where gDNA intensities showed a linear relationship with cDNA intensities in M versus A plots (M = log2(Cy5/Cy3) versus A = log2(Cy5xCy3)1/2) across all time points in both M and Y, as well as being below a two-fold change in gene expression values.  One hundred and two spots satisfied these criteria and were used as positive controls for per slide normalization process.

organism: Paracoccidioides brasiliensis

source_name: P. brasiliensis mycelial form, 5 days in culture

label_protocol: In brief, 100 μg of total RNA, in a volume of ≤ 10 μl, was used with the addition of 4 μg of Oligo-dT primer (5’ TTT TTT TTT TTT TTT TTT TTV N 3’) and nuclease-free water to a final volume of 15.4 μl.  This mixture was incubated at 70 C for 10 minutes and cooled on ice.  While on ice, 6 μl of 5X First Strand Buffer (Invitrogen), 3 μl 0.1 M DTT (dithiothreitol), 0.6 μl of dNTPs (25 mM dGTP, dATP, dCTP and 10 mM dTTP, Promega), 3 μl of Cy5-dUTP (Amersham Biosciences, Piscataway, NJ), and 400 U SuperScriptTM II Reverse Transcriptase (200 U/μl; Invitrogen) were added.  This mixture was incubated at 42 C for 1.5 h.  Reverse transcriptase activity was boosted by adding an additional 100 U of reverse transcriptase and incubation at 42 C for another 30 minutes.  RNA was degraded with 15 μl of 0.1 N NaOH and incubation at 70 C for 30 minutes.  NaOH was neutralized by the addition of 15 μl 0.1 N HCl and samples were maintained on ice prior to use.

growth_protocol:
Yeast (Y) cultures were maintained on modified McVeigh/Morton (MVM) agar slants (Restrepo & Jimenez, 1980) at 36 C and were transferred every 10-15 days.  Mycelial (M) cultures were maintained on MVM slants at ambient temperature and were transferred monthly.
Spent culture filtrate was used as growth supplement (2:1 ratio of fresh liquid MVM to spent culture filtrate) as previously described (Clemons et al., 1989; Stover et al., 1986) for the growth of liquid cultures M and Y prior to DNA and RNA extractions.
For total RNA extractions, one Y or two M five-day-old slants were used to inoculate 150 ml of supplemented liquid MVM media and incubated on a gyratory shaker at 150 rpm, at 36 C for Y or at ambient temperature for M, for 5, 8 or 14 days.  Liquid cultures were evaluated for contaminating organisms by microscopy and by plating samples on 5% sheep blood agar followed by incubation for 2-3 days at 36 C.

extract_protocol:
Cell disruption for total RNA extraction was performed as follows: fungal cells were collected by centrifugation (5 minutes at 500 x g), snap-frozen in liquid nitrogen, and 1 ml of TRIzol (Invitrogen Life Technologies, Carlsbad, CA) added per 1 g of pelleted cells.  After thawing, cells were mechanically disrupted with 0.5 mm zirconia/silica beads (Biospec) using a BeadBeater.  These homogenates were used in the extraction protocol provided by TRIzol’s manufacturer.
Removal of DNA copurified with total RNA was done in reactions containing 10 μg total RNA, 10 μl RQ1 DNase 10X reaction buffer, 10 units RQ1 RNase-free DNase, 40 units RNasin® Plus RNase Inhibitor (all from Promega, Madison, WI) and nuclease-free water (Sigma-Aldrich, St. Louis, MO) added to a final reaction volume of 100 μl.  Reactions were incubated at 37 C for one hour followed by incubation at 70 C for 30 minutes to inactivate the DNase.
The quantity and quality of the extracted RNA were assessed by A260nm/A280nm ratio and electrophoresis through a 1.5% agarose gel stained with ethidium bromide (presence of intact 18S and 28S ribosomal RNA bands) and visualized by UV transillumination at 302 nm.  Contaminating gDNA was removed using RNase-free DNase (RQ1 RNase-free DNase, Promega, Madison, WI) per the manufacturer’s instructions.

treatment_protocol: Snap frozen in liquid nitrogen for brief storage in -80 C prior to total RNA extraction.

tag: channel type

value: sample

tag: isolate

value: pb01 (atcc:MYA-826)

tag: morphologic form

value: mycelia

tag: growth

value: modified McVeigh/Morton liquid media for 5 days

molecule: genomic DNA

source_name: P. brasiliensis yeast, sheared genomic DNA

label_protocol: Cy3- or Cy5-labeled P. brasiliensis gDNA was synthesized from 250 ng of sheared gDNA using the BioPrime® Array CGH Genomic Labeling System (Invitrogen) following the manufacturer’s instructions.  Cy3-labeled gDNA was used as a control to facilitate comparisons between slides and data integration in future experiments (Gadgil et al., 2005; Talaat et al., 2002; Williams et al., 2006).  Cy5-labeled gDNA was used in self-to-self hybridizations along with Cy3-labeled gDNA during microarray validation procedures.

growth_protocol:
Yeast (Y) cultures were maintained on modified McVeigh/Morton (MVM) agar slants (Restrepo & Jimenez, 1980) at 36 C and were transferred every 10-15 days.  Mycelial (M) cultures were maintained on MVM slants at ambient temperature and were transferred monthly.
Spent culture filtrate was used as growth supplement (2:1 ratio of fresh liquid MVM to spent culture filtrate) as previously described (Clemons et al., 1989; Stover et al., 1986) for the growth of liquid cultures M and Y prior to DNA and RNA extractions.
For genomic DNA extractions, two five-day-old Y slants were used to inoculate 150 ml of supplemented liquid MVM media and incubated on a gyratory shaker at 150 rpm, at 36 C for 4 days.  Liquid cultures were evaluated for contaminating organisms by microscopy and by plating samples on 5% sheep blood agar followed by incubation for 2-3 days at 36 C.

extract_protocol:
Genomic DNA (gDNA) was extracted from Y collected from four-day-old liquid cultures (36 C, shaking at 150 rpm) using previously described methodology (McCullough et al., 2000).
Modifications to the original DNA extraction protocol included reduction of cell disruption time to 15 seconds at the high speed setting on a BeadBeater apparatus (Biospec Products, Inc., Bartlesville, OK) and precipitation of DNA using 100% ethanol (Gold Shield Chemical Co., Hayward, CA) following the RNase digestion step.
The quantity and quality of the extracted DNA were assessed using a spectrophotometric absorbance ratio (A260nm/A280nm) and by electrophoresis through a 0.8% agarose gel stained with ethidium bromide and visualized by ultraviolet (UV) transillumination.
Genomic DNA was sheared hydrodynamically into ~1.5 Kb fragments using a HydroShear® apparatus (Genomic Solutions, Ann Arbor, MI) as previously described (Oefner et al., 1996; Thorstenson et al., 1998).  Adequacy of DNA shearing was assessed by 1.5% agarose gel electrophoresis and visualized by UV after ethidium bromide staining.

treatment_protocol: None.

value: reference

value: yeast

value: modified McVeigh/Morton liquid media for 4 days


title: Paracoccidioides brasiliensis_mycelia_5 days in culture_flask1_rep2


title: Untreated THP-1 cells, biological rep1


title: Untreated THP-1 cells, biological rep2


title: Yeast_gene_order_S90_rep3

status: Public on May 07 2009

type: genomic

city: Chapel Hill

first: Jason

middle: D.

last: Lieb

state: NC

address: Department of Biology, #3280, Coker Hall

department: Biology and Carolina Center for Genome Sciences

institute: The University of North Carolina-Chapel Hill

description: Gene order S90 rep3

hyb_protocol: DNA was hybridized to the microarrays as previously described (see Iyer et al., 2001). In all cases, S288C was used as the reference for competitive hybridization.

scan_protocol: Images were acquired using a GenePix 4000B scanner and Genepix software (Axon Instruments)

data_processing: Data were uploaded to the UNC Microarray Database and retrieved as the log2 normalized ratio of (median intensity of sample pixels / median intensity of reference pixels). Only spots with a regression correlation >0.6 (i.e. those comprised of pixels with consistent ratio values). Spots that either failed from PCR or that were flagged in Genepix were not downloaded. Data were then z-score transformed such that the mean of all spots became 0 and the standard deviation became 1.

organism: Saccharomyces cerevisiae

source_name: genomic DNA S90

label_protocol: Samples and references were labeled using BioPrime Array CGH Genomic Labeling Module (Invitrogen) (see Gabriel et al., 2006)

extract_protocol: Twenty-milliliter cultures of each sample were grown in YPD medium (yeast extract 10g/L, peptone 20 g/L, and 2% dextrose) to OD600 greater than one. Cells were collected and resuspended in TE (700 μL of 200mM Tris, 50mM EDTA, pH 8) and frozen overnight. To digest cell walls, the cells were resuspended in 535 μL of 20mg/ml Zymolyase, 1.2 M Sorbitol, 20mM HEPES (pH 7.5) and incubated for 60 minutes at 37°C. Collected cells were resuspended in TE + 10 mg/ml RNaseA at 65°C for 30 minutes. 200 μL 5M potassium acetate was added and cells were incubated on ice for 1 hour. The lysed cells were then centrifuged at 14K rpm for 10 minutes to pellet debris (Sovall Biofuge Pico). Genomic DNA was ethanol precipitated from the supernatant and resuspended in 200 μL TE (pH 8). The solution was then sonicated to fragment DNA to an average size of ~ 500 bp. DNA was purified using YeaStar Genomic DNA Kit (Zymo Research, cat # D2002) and concentrations were determined by absorption spectroscopy with PicoGreen (Invitrogen)

tag: genomic DNA parent S90

source_name: genomic DNA S288C

tag: genomic DNA S288C (reference strain)


title: Yeast_gene_order_Y101_rep3

description: Gene order Y101 rep3

source_name: genomic DNA Y101

tag: genomic DNA parent Y101


title: Yeast_gene_order_55d_rep2

description: Gene order 55d rep2

source_name: genomic DNA 55d

tag: genomic DNA tetrad 55 spore d (tetrad derived from S90 x Y101)


title: Yeast_gene_order_S90_rep1

description: Gene order S90 rep1


title: Yeast_gene_order_Y101_rep1

description: Gene order Y101 rep1


title: Yeast_gene_order_Y101_rep2

description: Gene order Y101 rep2


title: Yeast_gene_order_S90_rep2

description: Gene order S90 rep2


title: Colon epithelium, Stat3flfl VilCre-, biolrep1


title: spleen 19

description: spleen

source_name: spleen

value: spleen


title: Yeast_gene_order_55d_rep1

description: Gene order 55d rep1


title: Yeast_gene_order_55c_rep2

description: Gene order 55c rep2

source_name: genomic DNA 55c

tag: genomic DNA tetrad 55 spore c (tetrad derived from S90 x Y101)


title: kidney 9

description: kidney

source_name: kidney

value: kidney


title: Yeast_gene_order_55c_rep1

description: Gene order 55c rep1


title: intestine large 10

value: intestine large


title: Yeast_gene_order_55b_rep2

description: Gene order 55b rep2

source_name: genomic DNA 55b

tag: genomic DNA tetrad 55 spore b (tetrad derived from S90 x Y101)


title: Yeast_gene_order_55b_rep1

description: Gene order 55b rep1


title: Yeast_gene_order_55a_rep1

description: Gene order 55a rep1

source_name: genomic DNA 55a

tag: genomic DNA tetrad 55 spore a (tetrad derived from S90 x Y101)


title: intestine large 11


title: Yeast_gene_order_36d_rep2

description: Gene order 36d rep2

source_name: genomic DNA 36d

tag: genomic DNA tetrad 36 spore d (tetrad derived from S90 x Y101)


title: Yeast_gene_order_55a_rep2

description: Gene order 55a rep2


title: Yeast_gene_order_36d_rep1

description: Gene order 36d rep1


title: Yeast_gene_order_36c_rep1

description: Gene order 36c rep1

source_name: genomic DNA 36c

tag: genomic DNA tetrad 36 spore c (tetrad derived from S90 x Y101)


title: Yeast_gene_order_36b_rep2

description: Gene order 36b rep2

source_name: genomic DNA 36b

tag: genomic DNA tetrad 36 spore b (tetrad derived from S90 x Y101)


title: Yeast_gene_order_36c_rep2

description: Gene order 36c rep2


title: kidney 8

description: kidney

tag: tissue


title: lymph nodes 13


title: Yeast_gene_order_36a_rep1

description: Gene order 36a rep1

source_name: genomic DNA 36a

tag: genomic DNA tetrad 36 spore a (tetrad derived from S90 x Y101)


title: Yeast_gene_order_36b_rep1

description: Gene order 36b rep1


title: Yeast_gene_order_36a_rep2

description: Gene order 36a rep2


title: Yeast_gene_order_32d_rep1

description: Gene order 32d rep1

source_name: genomic DNA 32d

tag: genomic DNA tetrad 32 spore d (tetrad derived from S90 x Y101)


title: Yeast_gene_order_32c_rep1

description: Gene order 32c rep1

source_name: genomic DNA 32c

tag: genomic DNA tetrad 32 spore c (tetrad derived from S90 x Y101)


title: Yeast_gene_order_32b_rep1

description: Gene order 32b rep1

source_name: genomic DNA 32b

tag: genomic DNA tetrad 32 spore b (tetrad derived from S90 x Y101)


title: Yeast_gene_order_32a_rep2

description: Gene order 32a rep2

source_name: genomic DNA 32a

tag: genomic DNA tetrad 32 spore a (tetrad derived from S90 x Y101)


title: cerebral cortex prefrontal 7

value: cerebral cortex prefrontal


title: Yeast_gene_order_32b_rep2

description: Gene order 32b rep2


title: cerebral cortex prefrontal 6


title: Yeast_gene_order_32a_rep1

description: Gene order 32a rep1


title: Yeast_gene_order_27c_rep2

description: Gene order 27c rep2

source_name: genomic DNA 27c

tag: genomic DNA tetrad 27 spore c (tetrad derived from S90 x Y101)


title: cerebellum 3

description: cerebellum

source_name: cerebellum

value: cerebellum


title: cerebral cortex 5

value: cerebral cortex


title: Yeast_gene_order_27d_rep1

description: Gene order 27d rep1

source_name: genomic DNA 27d

tag: genomic DNA tetrad 27 spore d (tetrad derived from S90 x Y101)

source_name: genomic DNA S288C


title: Yeast_gene_order_27b_rep1

description: Gene order 27b rep1

source_name: genomic DNA 27b

tag: genomic DNA tetrad 27 spore b (tetrad derived from S90 x Y101)

tag: genomic DNA S288C (reference strain)


title: Yeast_gene_order_27a_rep2

description: Gene order 27a rep2

source_name: genomic DNA 27a

tag: genomic DNA tetrad 27 spore a (tetrad derived from S90 x Y101)


title: Yeast_gene_order_27c_rep1

description: Gene order 27c rep1


title: Yeast_gene_order_27b_rep2

description: Gene order 27b rep2


title: Yeast_gene_order_23d_rep1

description: Gene order 23d rep1

source_name: genomic DNA 23d

tag: genomic DNA tetrad 23 spore d (tetrad derived from S90 x Y101)


title: Yeast_gene_order_23c_rep2

description: Gene order 23c rep2

source_name: genomic DNA 23c

tag: genomic DNA tetrad 23 spore c (tetrad derived from S90 X Y101)


title: Yeast_gene_order_23c_rep1

description: Gene order 23c rep1

tag: genomic DNA tetrad 23 spore c (tetrad derived from S90 x Y101)


title: Yeast_gene_order_27a_rep1

description: Gene order 27a rep1


title: Yeast_gene_order_23a_rep2

description: Gene order 23a rep2

source_name: genomic DNA 23a

tag: genomic DNA tetrad 23 spore a (tetrad derived from S90 x Y101)


title: Yeast_gene_order_23b_rep1

description: Gene order 23b rep1

source_name: genomic DNA 23b

tag: genomic DNA tetrad 23 spore b (tetrad derived from S90 x Y101)


title: cerebral cortex 4


title: Yeast_gene_order_23a_rep1

description: Gene order 23a rep1


title: Yeast_gene_order_23b_rep2

description: Gene order 23b rep2


title: Yeast_gene_order_7d_rep2

description: Gene order 7d rep2

source_name: genomic DNA 7d

tag: genomic DNA tetrad 7 spore d (tetrad derived from S90 x Y101)


title: Yeast_gene_order_7d_rep1

description: Gene order 7d rep1


title: Yeast_gene_order_7c_rep1

description: Gene order 7c rep1

source_name: genomic DNA 7c

tag: genomic DNA tetrad 7 spore c (tetrad derived from S90 x Y101)


title: Yeast_gene_order_7c_rep2

description: Gene order 7c rep2


title: Yeast_gene_order_7b_rep2

description: Gene order 7b rep2

source_name: genomic DNA 7b

tag: genomic DNA tetrad 7 spore b (tetrad derived from S90 x Y101)


title: Yeast_gene_order_7b_rep1

description: Gene order 7b rep1


title: Yeast_gene_order_27d_rep2

description: Gene order 27d rep2


title: Yeast_gene_order_23d_rep2

description: Gene order 23d rep2


title: Yeast_gene_order_32c_rep2

description: Gene order 32c rep2


title: cerebellum 2

description: cerebellum

tag: tissue


title: Yeast_gene_order_7a_rep2

description: Gene order 7a rep2

source_name: genomic DNA 7a

tag: genomic DNA tetrad 7 spore a (tetrad derived from S90 x Y101)


title: Adult-Planula3

status: Public on May 06 2009

city: San Francisco

first: Michael

last: DeSalvo

department: Department of Anesthesia

institute: UC San Francisco

description:
n/a
n/a

hyb_protocol: Dye-coupled cDNAs were cleaned (MinElute columns), and appropriate Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25 % SDS, 25 mM HEPES, and 3x SSC. The hybridization mixtures were boiled for 2 min at 99oC then allowed to cool at room temperature for 5 min. The cooled hybridization mixtures were pipetted under a mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 63oC. Microarrays were washed twice in 0.6x SSC and 0.01 % SDS followed by a rinse in 0.06x SSC and dried via centrifugation.

scan_protocol: All microarrays were scanned using an Axon 4000B scanner (Molecular Devices) where care was taken to balance photomultiplier tube (PMT) settings.

data_processing: Microarray data analysis -- The experiment followed a loop design in which all life stages (i.e. planula, polyp, adult) were directly compared against each other.  Hybridizations were performed in triplicate (n=3 for each developmental stage) and included dye swapping between technical replicates. Pre-processing of microarray intensity data was performed using TIGR TM4 software. Briefly, spot-finding was performed in SpotFinder 3.11 with background-subtracted median intensities being extracted. Using MIDAS 2.19, the data were first LOWESS normalized, and the dye swap pairs were collapsed; and secondly, the in-slide duplicates were collapsed. Resulting intensities in both channels (for nine total microarrays) were compiled into a spreadsheet. Genes were included in subsequent statistical analysis only if there were data in two out of three replicates for each developmental stage. Of 1310 possible genes, 1243 passed filtering criteria. The ratio between the fluorescence intensity of the two channels was used as input for BAGEL (Bayesian Analysis of Gene Expression Levels). The BAGEL software uses Bayesian probability to infer a relative expression level of each gene. An estimated mean and 95% credible interval of the relative level of expression of each gene is computed in each treatment and time point. We used the conservative gene-by-gene criterion of non-overlapping 95% credible intervals to regard a gene as differentially expressed.

label: Cy3, Cy5

organism: Orbicella faveolata

source_name: planula pool 3

label_protocol: Five µg of aRNA per sample were primed with 5 µg/µL random nonamer for 10 min at 70oC.  Reverse transcription (RT) lasted for 2 hr at 50oC using a master mix containing a 4:1 ratio of aminoallyl-dUTP to TTP. Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10 µL 0.5 M EDTA and 10 µL 1 M NaOH for 15 min at 65oC. After hydrolysis, RT reactions were cleaned using MinElute Reaction Purification columns (Qiagen). Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 12 µL DMSO, and the coupling reactions lasted for 2 hr at room temperature in the dark.

extract_protocol: Total RNA from frozen coral tissues was isolated using Qiazol lysis reagent (Qiagen) following product specifications. Both adult and larval tissues were homogenized using a pre-chilled mortar and pestle. Frozen coral powder was transferred directly to Qiazol. Two chloroform extractions were performed, followed by isopropanol precipitation and two washes in 80% ethanol. RNA pellets were re-dissolved in nuclease-free water and cleaned further with RNeasy Mini columns (Qiagen). RNA quantity and integrity were assessed with a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. All RNA samples were amplified using the MessageAmp II aRNA kit (Ambion) with 1 µg of total RNA as input.

tag: developmental stage

value: planula

source_name: adult fragment 3

value: adult


title: Polyp-Planula1

description:
n/a
n/a

source_name: planula pool 1

source_name: polyp pool 1

value: polyp


title: Yeast_gene_order_32d_rep2

description: Gene order 32d rep2

source_name: genomic DNA 32d

tag: genomic DNA tetrad 32 spore d (tetrad derived from S90 x Y101)


title: Polyp-Planula2

description:
n/a
n/a

source_name: planula pool 2

source_name: polyp pool 2


title: Polyp-Planula3

description:
n/a
n/a

source_name: polyp pool 3


title: Lung-control

city: Genoa

first: Alberto

last: Izzotti

address: A. Pastore, 1

department: Dept. of Health Sciences

country: Italy

institute: University of Genoa

hyb_protocol: Microarray were hybridized in 6X SSPE/30% formamide at 25°C for 18h, washed in 0,75XTNT buffer at 37 for 40 min, and processed using direct detection of the biotin-containing transcript by streptavidin-Alexa647 conjugate. T

scan_protocol: The processed slides were scanned by using an Axon 4000B microarray Scanner, with the laser set at 635 nm and Power 80% and the photomultiplier set at 70% with a scan resolution of 10 µm

data_processing: After local background subtraction, raw data were log transformed normalized and analyzed by GeneSpring software version 7.2. Expression data were median centered using the GeneSpring normalization option, which normalizes both per gene and per array. Comparison between ECS and sham were done by evaluating the fold variation of the mean value of quadruplicate data generated for each miRNA. In addition, the statistical significance of the differences was evaluated by using the GeneSpring ANOVA tool and Bonferroni multiple testing correction. Correlations between rodent and human miRNA were evaluated by simple regression analysis using the StatView software.

label: Biotin

organism: Rattus sp.

source_name: Lung

label_protocol: Five µg of total RNA was reverse-transcribed using a reaction mix containing 1µg of (3'(N)8-(A)12-biotin-(A)12-biotin 5') oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. Four µl of 5X first-strand buffer, 2 volumes of DTT 0,1M, 1µl of 10 mM dNTPs mix and 1µl Superscript II RNaseH reverse transcriptase (200 U/µl) were added. The samples were incubated for 90 min at 37°C. To denature the RNA/DNA hybrids and degrade RNA templates a mixture of  3,5 µl of 0,5M NaOH/ 50mM EDTA were added to 20 µl of first reaction mix. Five µl of 1M Tris-HCl pH7,6 were added to neutralize the reaction mix, and the labeled targets were stored at -80°C until hybridization.

growth_protocol: Sixteen Sprague-Dawley rats, were either exposed to ECS for 4 weeks or kept in filtered air for the same period of time (sham)

extract_protocol: The lungs were collected, immersed in an RNA stabilizing buffer and frozen at -80°C

tag: strain

value: Sprague-Dawley rats


title: Adult-Planula2

description:
n/a
n/a

source_name: adult fragment 2


title: Lung-ECS


title: Yeast_gene_order_7a_rep1

description: Gene order 7a rep1

hyb_protocol: DNA was hybridized to the microarrays as previously described (see Iyer et al., 2001).  In all cases, S288C was used as the reference for competitive hybridization.

source_name: genomic DNA S288C


title: Wild type Salmonella vs Salmonella harbouring pTrc99A(+LacI)

city: Bangalore

first: Dipshikha

last: Chakravortty

state: Karnataka

address: C.V.Raman AVENUE

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description: Grid and spot alignment is performed by using Scanarray microarray analysis software form PerkinElmer.

hyb_protocol: 1. Carefully pipette entire 40 ul sample mixture onto the middle of the array surface. Do not allow direct contact of the array surface with pipette tip, as this may scratch the array surface. Avoid creation of air bubbles in the hybridization buffer. 2. Gently overlay the cover slip onto the solution on the array by positioning the cover slip at one end of the array and lowering it down until it is in contact with the hybridization solution. Be sure the solution covers the entire array footprint. Small bubbles will not to lose hybridization. 3. Pipet 500 ul of 2X SSC onto a flat, folded dust free tissue. This is sufficient to maintain the humidity inside the hybridization chamber. 4. Very carefully, place the microarray slide over the damp tissue and seal the cap tightly. Be very careful that the cover slip does not slip off. Be sure that the array does not touch the tissue as this may remove hybridization solution from the array surface through capillary action. 5. Place the tube in a 650 C incubator. Ensure the microarray, now enclosed in the tube, is level and stable in the incubator. Allow the hybridization to proceed overnight (18 hours) at this temperature.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Scan data (Raw data) is analyzed using GeneSpring GX v7.3. Per spot per chip lowess normalization was done. To account for dye swap, the signal channel and control channel measurements for sample(s) 2 were reversed. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Biological analysis was done using Genotypic's Biointerpreter software.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Wild type Salmonella

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA

extract_protocol: RNeasy Mini Kit (QIAGEN)

tag: cell type

value: wild type

source_name: Wild type Salmonella harbouring pTrc99A(+LacI)

value: wild type Salmonella transformed with pTrc99A(+LacI)


title: Salmonella harbouring pTrc99A(+LacI) vs Wild type Salmonella


title: Wild type Salmonella vs Salmonella harbouring pTrc99A(-LacI)

source_name: Wild type Salmonella harbouring pTrc99A(-LacI)

value: wild type Salmonella transformed with pTrc99A(-LacI)


title: Salmonella harbouring pTrc99A(-LacI) vs Wild type Salmonella


title: NOD/scid mouse lung 10 h after IV infusion of human MSCs (430 2.0)

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

description:
Cultured adult human MSCs.
NOD/scid mouse lung 10h after IV infusion of hMSCs.

hyb_protocol: Labeled cRNA was hybridized for 16 hours at 45C onto the MG-430 2.0 array (Affymetrix). After washing, the array was stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR), amplified with biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA) and stained again with streptavidin-phycoerythrin.

scan_protocol: The array was scanned for fluorescence (GeneChip Scanner 3000, Affymetrix) using the GeneChip Operating software 1.0 (GCOS, Affymetrix)

data_processing: The array was scaled to target value of 500.

organism:
Homo sapiens
Mus musculus

source_name: NOD/scid mouse lung 10 h after IV infusion of hMSCs

label_protocol: 7 μg of total RNA was used to synthesize double-stranded cDNA (Superscript Choice System, GIBCO /BRL).  The double-stranded cDNA was purified by phenol/chloroform extraction (Phase Lock Gel, Eppendorf, Hamburg, Germany) and concentrated by ethanol precipitation. In vitro transcription was used to produce biotin-labeled cRNA (BioArray HighYield RNA Transcription Labeling Kit; Enzo Diagnostics, Farmingdale, NY).  The biotinylated cRNA was then cleaned (RNeasy Mini Kit) and fragmented.

growth_protocol: Human MSCs were isolated from 1– 4-ml bone marrow aspirates taken from the iliac crest of normal adult donors. Nucleated cells were isolated with a density gradient and resuspended in complete culture medium (CCM) consisting of alpha-minimal essential medium, 17% fetal bovine serum (FBS), 100 units/ml penicillin, 100 ug/ml streptomycin, and 2 mM L-glutamine. All of the nucleated cells were plated in 20 ml of medium in a 175-cm2 culture dish and incubated at 37°C with 5% CO2. After 24 hours, nonadherent cells were discarded, and adherent cells were thoroughly washed twice with phosphate-buffered saline (PBS). The cells were incubated 4 –11 days until approximately 70% confluent, harvested with 0.25% trypsin and 1 mM EDTA for 5 minutes at 37°C, and replated at 50 cells/cm2 in an intercommunicating system of cultureflasks. The cells were incubated 7–10 days until approximately 70% confluent, harvested with trypsin/EDTA, suspended at 1 million cells/ml in 5% dimethyl sulfoxide and 30% FBS, and frozen in 1-ml aliquots at -80°C overnight and then placed in liquid nitrogen (passage 1 cells). A frozen vial of MSCs was then thawed and cells were plated in a 145-cm2 culture dish in CCM. After 24-hour incubation at 37°C and 5% CO2, the medium was removed, cells were washed with PBS, and adherent viable cells were harvested with trypsin/EDTA. Recovered passage 1 MSCs were then plated at 100 cells/cm2 on 15cm plastic dishes. Cells were cultured for 7 days in CCM. About 2 X 106 hMSCs were infused IV into NOD/scid mouse and lung RNA was isolated 10h after infusion.

extract_protocol: RNA was isolated with Trizol (Invitrogen) and cleaned by RNeasy Mini Kit (Qiagen).

tag: sample type

value: mixture of cultured adult human MSCs and NOD/scid mouse lung


title: Human MSCs added to the NOD/scid mouse lung in vitro (430 2.0)

description:
Cultured adult human MSCs.
NOD/scid mouse lung.
In vitro mixing of the tissues.

source_name: In vitro mix of human MSCs and NOD/scid mouse lung

growth_protocol: Human MSCs were isolated from 1– 4-ml bone marrow aspirates taken from the iliac crest of normal adult donors. Nucleated cells were isolated with a density gradient and resuspended in complete culture medium (CCM) consisting of alpha-minimal essential medium, 17% fetal bovine serum (FBS), 100 units/ml penicillin, 100 ug/ml streptomycin, and 2 mM L-glutamine. All of the nucleated cells were plated in 20 ml of medium in a 175-cm2 culture dish and incubated at 37°C with 5% CO2. After 24 hours, nonadherent cells were discarded, and adherent cells were thoroughly washed twice with phosphate-buffered saline (PBS). The cells were incubated 4 –11 days until approximately 70% confluent, harvested with 0.25% trypsin and 1 mM EDTA for 5 minutes at 37°C, and replated at 50 cells/cm2 in an intercommunicating system of cultureflasks. The cells were incubated 7–10 days until approximately 70% confluent, harvested with trypsin/EDTA, suspended at 1 million cells/ml in 5% dimethyl sulfoxide and 30% FBS, and frozen in 1-ml aliquots at -80°C overnight and then placed in liquid nitrogen (passage 1 cells). A frozen vial of MSCs was then thawed and cells were plated in a 145-cm2 culture dish in CCM. After 24-hour incubation at 37°C and 5% CO2, the medium was removed, cells were washed with PBS, and adherent viable cells were harvested with trypsin/EDTA. Recovered passage 1 MSCs were then plated at 100 cells/cm2 on 15cm plastic dishes. Cells were cultured for 7 days in CCM. About 1 X 106 hMSCs were added to lung from control mouse (NOD/scid) just before homogenization.


title: NOD/scid mouse lung (430 2.0)

description: NOD/scid mouse lung

source_name: NOD/scid mouse lung

tag: genotype

value: NOD/scid

value: lung


title: Adult-Planula1

description:
n/a
n/a

source_name: adult fragment 1


title: Adult-Polyp2

description:
n/a
n/a


title: Adult-Polyp1

description:
n/a
n/a


title: Adult-Polyp3

description:
n/a
n/a

source_name: adult fragment 3


title: si cyto 1

city: Boston

first: Peter

middle: A

last: Burke

state: MA

address: 850 Harrison Avenue, Dowling 2 South

department: Surgery

institute: Boston University School of Medicine

description: Gene Expression In Cytokine & HNF4 si treated HepG2 Cells

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on the GeneChip Human Genome U133 A 2.0 (Affymetrix, Santa Clara, CA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Microarray data were quantified and normalized using Affymetrix MicroArray Suite (MAS) 5.0

source_name: Cytokine & HNF4 si treated HepG2 Cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: HepG2 cells were grown in Dulbecco Modified Eagle Medium supplemented with penicillin (100 units/ml), streptomycin (100 ug/ml), and 10% heat-inactivated fetal bovine serum at 37° C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The inflammatory response in HepG2 cells was stimulated with a cytokine mixture containing 1 ng/ml of recombinant human IL-1β, 10 ng/ml of IL-6, and 10 ng/ml of TNF-α in serum-free medium for 18 h. Knock-down of HNF-4α in HepG2 cells was transfected with shRNA (HNF-4α shRNA and non-specific control shRNA) using the Nucleofector (Amaxa Biosystem) following the manufacturer's instructions. Twenty-four hours after transfection, the cells were placed in serum-free medium for 5 h and then either treated or untreated with cytokines for 18 h.

tag: hnf4 si rna treatment

value: treated

tag: cytokine treatment


title: si cyto 4


title: si 4

description: Gene Expression In HNF4 si treated HepG2 Cells

source_name: HNF4 si treated HepG2 Cells

value: untreated


title: si 3


title: cyto 3

description: Gene Expression In Cytokine treated HepG2 Cells

source_name: Cytokine treated HepG2 Cells


title: si cyto 3


title: si 2


title: cyto 4


title: cyto 1


title: cyto 2


title: control 3

description: Gene Expression In Untreated HepG2 Cells

source_name: Untreated HepG2 Cells


title: si cyto 2


title: Weakly metastatic line SCP43

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

department: Molecular Biology

institute: Princeton University

description:
Bone metastatic signature: negative
Lung metastatic signature: negative

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Genespring GX 7.3 Expression Analysis using Per Chip (normalize to 50th percentile) and Per Gene (normalize to median) normalization methods.

source_name: Weakly metastatic line SCP43

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: The sublines and their fusion variants were maintained in DMEM with 10% FBS and antibiotics supplemented with appropriate selective drugs.

extract_protocol: Total RNA extracted using Qiagen RNAeasy mini kit following manufacturer's instructions.

treatment_protocol: Cells were grown to sub-confluency before harvesting RNA.

tag: Tissue

value: breast cancer


title: control 1


title: si 1


title: control 4


title: Weakly metastatic line SCP32

source_name: Weakly metastatic line SCP32


title: Weakly metastatic line SCP28

source_name: Weakly metastatic line SCP28


title: Weakly metastatic line SCP4

source_name: Weakly metastatic line SCP4


title: control 2


title: Lung metastatic line 4175

description:
Bone metastatic signature: negative
Lung metastatic signature: positive

source_name: Lung metastatic line 4175


title: Weakly metastatic line SCP6

source_name: Weakly metastatic line SCP6


title: Lung metastatic line 4180

source_name: Lung metastatic line 4180


title: Weakly metastatic line SCP3

source_name: Weakly metastatic line SCP3


title: Lung metastatic line 4173

source_name: Lung metastatic line 4173


title: Lung metastatic line 3481

source_name: Lung metastatic line 3481


title: Lung metastatic line 4142

source_name: Lung metastatic line 4142


title: Bone metastatic line SCP25

description:
Bone metastatic signature: positive
Lung metastatic signature: negative

source_name: Bone metastatic line SCP25


title: Bone metastatic line SCP46

source_name: Bone metastatic line SCP46


title: bladder 1

description: bladder

source_name: bladder

value: bladder


title: Bone metastatic line SCP14

source_name: Bone metastatic line SCP14


title: Hetero-fused line BLm-DRUG, clone 8

description:
Bone metastatic signature: positive
Lung metastatic signature: positive

source_name: Hetero-fused line BLm-DRUG, clone 8


title: Self-fused line BBm

source_name: Self-fused line BBm


title: Hetero-fused line BLm-DRUG, clone 18

source_name: Hetero-fused line BLm-DRUG, clone 18


title: Cell fusion partner line Bm

source_name: Cell fusion partner line Bm


title: Hetero-fused line BLm-FACS

source_name: Hetero-fused line BLm-FACS


title: Hetero-fused line BLm-DRUG, clone 12

source_name: Hetero-fused line BLm-DRUG, clone 12


title: Bone metastatic line 1833

source_name: Bone metastatic line 1833


title: Self-fused line LLm

source_name: Self-fused line LLm


title: CN34 BrM2c

city: New York

first: Paula

middle: D

last: Bos

state: NY

address: 1275 York Avenue

department: Cancer Biology

institute: Memorial Sloan Kettering Cancer Institute

description: Breast cancer in vivo selection of brain metastatic variants to identify gene expression changes associated with brain metastasis

hyb_protocol: according to manufacturer

scan_protocol: according to manufacturer on  GC3000 scanner

data_processing: Global intensity was targetted to 500. Data were extracted using GCOS 1.3

label: biotin-labeled cRNA

source_name: Breast cancer pleural effusion

label_protocol: standard Affymetrix labeling protocol (Invitrogen+Enzo)

extract_protocol: Rneasy mini kit Qiagen

tag: Breast cancer pleural effusion, brain metastatic isolate


title: Cell fusion partner line Lm

source_name: Cell fusion partner line Lm


title: Hetero-fused line BLm-DRUG

source_name: Hetero-fused line BLm-DRUG


title: Bone metastatic line SCP20

source_name: Bone metastatic line SCP20


title: CN34 BrM2a


title: CN34 BrM1a


title: CN34 BrM2b

tag: Breast cancer pleural effusion, brain metastatic variant


title: MDA-MB-231 Parental

source_name: Breast cancer cell line

tag: Breast cancer  parental cell line


title: MDA-MB-231 BrM3b

source_name: MDA-MB-231 breast cancer cell line brain metastatic variant


title: MDA-MB-231 Parental_AM_B

source_name: MDA-MB-231 Breast cancer cell line

tag: MDA-MB-231 breast cancer parental cell line


title: MDA-MB-231


title: MDA-MB-231 BrM2b

tag: MDA-MB-231 breast cancer cell line brain metastatic variant


title: MDA-MB-231 BrM1a


title: MDA-MB-231 BrM2a

source_name: MDA-MB-231 breast cancer brain metastatic variant


status: Public on May 05 2009

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_time point twenty-four negative control rep 4

hyb_protocol: ~1ug label and fragmented applied for 16hrs 40OC

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Francisella tularensis subsp. tularensis SCHU S4

label_protocol: RNA amplification step was introduced as follows: all RNA samples that were generated from F. tularensis SchuS4-infected and noninfected BMMs were randomized on a single 96-well plate and the MessageAmp II-Bacteria kit (Ambion, Foster City, CA) was used to amplify 0.5 to 1 μg of mixture of F. tularensis and BMM RNAs according to manufacturer's instructions. Briefly, RNAs were concentrated to 5 μl, denatured for 10 min at 70°C, polyadenylated using E.coli polyA polymerase for 15 min at 37°C, and reverse transcribed for 2 h at 42°C using ArrayScript and polydT primer with a T7 tail.  Second strand synthesis was performed immediately after first strand cDNA synthesis for 2 h at 16°C. Purified cDNA was mixed with 75 nmol of biotin-16-UTP (Roche Applied Science, Mannheim, Germany) and concentrated to 18 μl. Biotin-labeled complementary pathogen-host RNA was amplified at 37°C in an overnight 40 μl in vitro transcription reaction. The amount of target consisting of macrophage and F. tularensis cRNAs was determined by Absorbance measurements at 260 nm. The quality and the size of the amplified targets were determined on a Agilent 2100 Bioanalyzer using the Pico analysis kit (Agilent Technologies, Palo Alto, CA). The amount of F. tularensis cRNA was estimated by quantitative RT-PCR of the FTT0243 locus, as described below, using a standard curve method (Applied Biosystems, Foster City, CA). F.tularensis RNA extracted from a bacterial suspension in TSB-C was used for the RNA standard curve.

growth_protocol: Bone marrow cells were isolated from femurs of 6-10 week-old, C57BL/6J female mice (Jackson Laboratories, Bar Harbor, ME, USA) and differentiated into macrophages for 5 days at 37°C and 7% CO2, in 1g/L glucose Dulbecco's Modified Eagle Medium (DMEM, Invitrogen) supplemented with 10% fetal bovine serum (FBS, Invitrogen), 10% L-conditioned medium {de Chastellier, 1993 #28}, and 2 mM L-glutamine in non tissue culture-treated Petri dishes. After 5 days, loosely adherent BMMs were washed with PBS, harvested by incubation in chilled cation-free PBS on ice for 10 min, resuspended in complete medium and replated in either 6-, 12- or 24-well cell culturetreated plates at a density of 1x106, 5x105 or 1x105 macrophages/well, respectively. BMMs were further incubated at 37°C under 7% CO2 atmosphere for 48 h, with replenishing complete medium 24 h before infection. For infections, bacterial suspensions were diluted in complete medium and 1.5, 1 or 0.5 ml was added to chilled BMMs at an appropriate multiplicity of infection (MOI) of 50, unless stated otherwise. Bacteria were centrifuged onto macrophages at 400 x g for 10 min at 4°C, and infected BMMs incubated for 20 min at 37°C under 7% CO2 atmosphere including an initial, rapid warm up in a 37°C water bath to synchronize bacterial uptake. Infected BMMs were 23 then washed 5 times with DMEM to remove extracellular bacteria, incubated for an additional 60 min in complete medium containing 100 μg/ml gentamicin to kill extracellular bacteria and thereafter in gentamicin-free medium until processing.

extract_protocol: At each time point, samples were washed 3 times with sterile PBS to remove residual extracellular bacteria, and both BMMs and bacteria were lysed directly in the wells by the addition of 1 ml TRIzol (Invitrogen, Carlsbad, CA) and pipetting 10 times. Samples were transferred to microtubes, 200 ìl chloroform were added, vials were vortexed, and centrifuged at 16,000 x g for 15 min. The RNA-containing aqueous phase was collected from each sample and passed through a Qiashredder column (Qiagen, Valencia, CA) at 21,000 x g for 2 min.

treatment_protocol: BMMs seeded in 12-well plates were infected with Schu S4 at a MOI of either 200 (0, 1, 2 and 4 h time points), 50 (8, 12 h time points) or 25 (16 and 24 h time points). The use of different MOIs in this experimental design was required to recover sufficient amount of bacterial RNA at all time points analyzed but did not affect the timing of the Francisella intracellular cycle, therefore generating biologically comparable samples. Time zero samples were generated by adding bacteria (MOI 200; 108/well) directly to BMMs that had been washed with PBS, followed by the immediate addition of lysis buffer, as described below. Uninfected controls were generated at both 0 and 24h post infection.

tag: Schu 4


description: Gene expression data from_time point twenty-four negative control rep 2


title: MDA-MB-231 Parental_AM

source_name: Breast cancer cell line MDA-MB-231

tag: Breast cancer cell line MDA-MB-231 parental


title: time point zero negative control rep4

description: Gene expression data from_time point zero negative control rep4

source_name: time point zero negative control rep4


title: time point zero negative control rep3

description: Gene expression data from_time point zero negative control rep3

source_name: time point zero negative control rep3


title: time point twenty-four rep 3

description: Gene expression data from_time point twenty-four rep 3

source_name: time point twenty-four rep 3


title: time point zero negative control rep1

description: Gene expression data from_time point zero negative control rep1

source_name: time point zero negative control rep1


title: CN34 Parental

tag: Breast cancer pleural effusion, parental population isolated from patient


title: time point four rep 3

description: Gene expression data from_time point four rep 3

source_name: time point four rep 3


title: time point sixteen rep 3

description: Gene expression data from_time point sixteen rep 3

source_name: time point sixteen rep 3


description: Gene expression data from_time point twenty-four negative control rep 1


title: time point sixteen rep 1

description: Gene expression data from_time point sixteen rep 1

source_name: time point sixteen rep 1


title: time point twenty-four rep 2

description: Gene expression data from_time point twenty-four rep 2

source_name: time point twenty-four rep 2


title: time point eight rep 1

description: Gene expression data from_time point eight rep 1

source_name: time point eight rep 1


title: time point zero negative control rep2

description: Gene expression data from_time point zero negative control rep2

source_name: time point zero negative control rep2


title: time point sixteen rep 2

description: Gene expression data from_time point sixteen rep 2

source_name: time point sixteen rep 2


title: time point two rep 3

description: Gene expression data from_time point two rep 3

source_name: time point two rep 3


title: time point two rep 2

description: Gene expression data from_time point two rep 2

source_name: time point two rep 2


title: time point four rep 2

description: Gene expression data from_time point four rep 2

source_name: time point four rep 2


title: time point one rep 1

description: Gene expression data from_time point one rep 1

source_name: time point one rep 1


title: time point two rep 1

description: Gene expression data from_time point two rep 1

source_name: time point two rep 1


title: time point one rep 2

description: Gene expression data from_time point one rep 2

source_name: time point one rep 2


title: 13483894 - pBIN18h vs Ovex18h

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties.

hyb_protocol: Ovex18h Cy5 / pBIN18h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: leaf - Media : soil hygrometry : 70% Temperature : 20°C Light : 12/12h

treatment_protocol: Name:Paraquat - time course study - abiotic stress,paraquat:. Paraquat (10 (u)M) was infiltrated in leaves with needleless syringe. each genotype at 0 (T0), 4 (T1) and 18 (T2) hours after Paraquat infiltration.

value: arabidopsis thaliana (columbia)

tag: age

value: dev.stage (boyes et al. plant cell 2001):boyes:5.10


title: time point four rep 1

description: Gene expression data from_time point four rep 1

source_name: time point four rep 1


title: 13483895 - Ovex18h vs pBIN18h

hyb_protocol: pBIN18h Cy5 / Ovex18h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13500961 - pBIN18h vs Asense18h

hyb_protocol: Asense18h Cy5 / pBIN18h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (columbia)  mutant (asense:silenced for expression of PLP2, a patatin-like LAH (At2g26560))

value: dev.stage (Boyes et al. Plant Cell 2001):boyes:5.10


title: time point zero rep 1

description: Gene expression data from_time point zero rep 1

source_name: time point zero rep 1


title: time point one rep 3

description: Gene expression data from_time point one rep 3

source_name: time point one rep 3


title: time point twenty-four rep 1

description: Gene expression data from_time point twenty-four rep 1

source_name: time point twenty-four rep 1


title: time point zero rep 3

description: Gene expression data from_time point zero rep 3

source_name: time point zero rep 3


title: 13366279 - pBIN4h vs Ovex4h

hyb_protocol: Ovex4h Cy5 / pBIN4h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: time point zero rep 2

description: Gene expression data from_time point zero rep 2

source_name: time point zero rep 2


description: Gene expression data from_time point twenty-four negative control rep 3


title: 13483889 - pBIN18h vs pBINT0

hyb_protocol: pBINT0 Cy5 / pBIN18h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366282 - Ovex4h vs pBIN4h

hyb_protocol: pBIN4h Cy5 / Ovex4h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13483877 - Asense18h vs pBIN18h

hyb_protocol: pBIN18h Cy5 / Asense18h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13483890 - pBINT0 vs pBIN18h

hyb_protocol: pBIN18h Cy5 / pBINT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC12-ND6 t=48 hrs rep6

city: Washington

first: Anne

last: Chiaramello

state: DC

address: 2300 I Street N.W. Ross Hall 427

department: Anatomy and Regenerative Biology

institute: George Washington University Medical Center

description: Gene Expression upon NeuroD6 overexpression in the absence of serum

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G

data_processing: Signal intensities were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Microarray data were generated using the Affymetrix GCOS program.  CEL files were generated and data normalization was performed using GC-RMA and per gene normalization to median.

organism: Rattus norvegicus

source_name: PC12 rat pheochromocoma

label_protocol: Biotin-labeling of antisense cRNA was performed using 15 µg of total RNA and the Bioarray High Yield RNA transcript labeling kit (Affymetrix)  and labeled cRNA was fragmented by metal-induced hydrolysis.

growth_protocol: Cells  were seeded on Collagen I-coated plates and grown at 37 C in F-12K medium supplemented with 15% horse and 2.5% fetal bovine serum, based on ATCC recommendations.

extract_protocol: Total RNA was isolated using the RiboPure kit from Applied Biosystem

treatment_protocol: When mentioned, cells were grown in the absence of serum for 48 hours to test  NeuroD6-mediated neuronal survival.

value: Stable NeuroD6 overexpressing PC12 cell line

tag: activity

value: responsive to NGF

tag: phenotype

value: neuronal


title: 13366277 - pBIN4h vs Asense4h

hyb_protocol: Asense4h Cy5 / pBIN4h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: strain


title: 13301349 - Ovex48h vs pBIN48h

hyb_protocol: pBIN48h Cy5 / Ovex48h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: leaf - Media : soil Hygrometry : 70% Temperature : 20°C Light : 12/12h

treatment_protocol: Name:Botrytis cinerea infection - time course study - pathogen infection,botrytis cinerea:time 0hour .

value: 7weekdev.stage (Boyes et al. Plant Cell 2001):boyes:5.10

value: arabidopsis thaliana (columbia)  mutant (ovex:PLP2-overexpressor)


title: 13366276 - pBIN4h vs pBINT0

hyb_protocol: pBINT0 Cy5 / pBIN4h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366278 - Asense4h vs pBIN4h

hyb_protocol: pBIN4h Cy5 / Asense4h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC12-ND6 t=48 hrs rep5

tag: cell type


title: 13366275 - pBINT0 vs pBIN4h

hyb_protocol: pBIN4h Cy5 / pBINT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC12-ND6 t=48 hrs rep4


title: PC12-ND6 t=48 hrs rep2


title: PC12-ND6 t=48 hrs rep3


title: 13301350 - pBINT0 vs OvexT0

hyb_protocol: OvexT0 Cy5 / pBINT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC12-ND6 t=0 rep6

description: Gene Expression upon NeuroD6 overexpression in the presence of serum


title: PC12-ND6 t=0 rep4


title: 13301348 - pBIN48h vs Ovex48h

hyb_protocol: Ovex48h Cy5 / pBIN48h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC12-ND6 t=0 rep5


title: 13301347 - Asense48h vs pBIN48h

hyb_protocol: pBIN48h Cy5 / Asense48h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 12997968 - seT0 vs pBINT0

hyb_protocol: pBINT0 Cy5 / seT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: leaf - media : soil hygrometry : 70% temperature : 20°C light : 12/12h

value: arabidopsis thaliana (columbia)  mutant (seplp2:PLP2-overexpressor)


title: PC12-ND6 t=0 rep2


title: 13300953 - pBINT0 vs pBIN48h

hyb_protocol: pBIN48h Cy5 / pBINT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13300954 - pBIN48h vs pBINT0

hyb_protocol: pBINT0 Cy5 / pBIN48h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC12-ND6 t=48 hrs rep1


title: 13301351 - OvexT0 vs pBINT0

hyb_protocol: pBINT0 Cy5 / OvexT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC12-ND6 t=0 rep3


title: PC12 control rep5

description: Gene expression from undifferentiated control PC12 cells

value: tumor cells from adrenal gland

tag: gender

value: male


title: 12997969 - pBINT0 vs seT0

hyb_protocol: seT0 Cy5 / pBINT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC12 control rep6


title: PC12 control rep3


title: PC12 control rep1


title: 13301352 - pBIN48h vs Asense48h

hyb_protocol: Asense48h Cy5 / pBIN48h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC12 control rep4


title: 13190059 - siT48 vs pBINT48

hyb_protocol: pBINT48 Cy5 / siT48 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: leaf - media : soil hygrometry : 70% temperature : 20°C Light : 12/12h

value: arabidopsis thaliana (columbia)  mutant (siplp2:silenced for expression of PLP2, a patatin-like LAH (At2g26560))


title: PC12 control rep2


title: 12997967 - pBINT24 vs seT24

hyb_protocol: seT24 Cy5 / pBINT24 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC12-ND6 t=0 rep1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.


title: 12997959 - siT24 vs pBINT24

hyb_protocol: pBINT24 Cy5 / siT24 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 12997960 - pBINT24 vs siT24

hyb_protocol: siT24 Cy5 / pBINT24 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 12997963 - seT24 vs pBINT24

hyb_protocol: pBINT24 Cy5 / seT24 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CN34 Parental replicate

description: Breast cancer in vivo selection of brain metastatic variants to identify gene expression changes associated with brain metastasis

hyb_protocol: according to manufacturer

source_name: Breast cancer pleural effusion


title: Rhesus macaque cerebellum, biological rep 3

city: Iowa City

first: Yi

last: Xing

state: IA

address: 3294 CBRB, 285 Newton Rd

department: Internal Medicine, Biomedical Engineering

institute: University of Iowa

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Human Exon Junction arrays (HJAY arrays) according to manufacturer’s protocols at the University of Iowa DNA facility.

scan_protocol: Hybridized Affymetrix Human Exon Junction arrays (HJAY arrays) were scanned following the manufacturer’s protocols at the University of Iowa DNA facility.

data_processing: Raw image files were processed using Affymetrix GCOS software to generate CEL data files. The GeneBASE algorithm (Kapur et al., 2007, Genome Biol 8:R82) was used to produce the expression values, with minor modifications. Exon array expression indexes were calculated by the JETTA program using perfect-match probes shared between human, chimpanzee and rhesus macaque genomes.

organism: Macaca mulatta

source_name: rhesus macaque cerebellum

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix Human Exon Junction arrays (HJAY arrays) was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).  Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).

tag: tissue

value: cerebellum

value: female

value: 8 years


title: Rhesus macaque cerebellum, biological rep 2


title: Rhesus macaque cerebellum, biological rep 1

value: 11 years


title: STAT3+/+ MEF cell line tretated with OSM 03

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

description: Spontaneously immortalized STAT3+/+ MEFs were grown in DMEM supplemented with 10% heat-inactivated FCS, 2 mM L-glutamine, 100 U/ml of penicillin, 100 μg/ml of streptomycin and maintained at 37°C in a 5% CO2 atmosphere. Cells were treated with Oncostatin M (OSM) (R&D Systems Inc.) at a final concentration of 20 ng/ml for 30 minutes.

hyb_protocol: cRNA was hybridized on MGU74A v2 Affymetrix DNA chip according to the Affymetrix protocol.

scan_protocol: The chip was scanned with Affymetrix scanner, using default parameters.

data_processing: Microarray quality control and feature selection was done using Bioconductor . The presence of hybridization/construction artifacts was evaluated with the fitPLM function (Bioconductor package affyPLM). The probes (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by mean of GCRMA (Bioconductor package gcrma), and normalization was done according to quantiles method.

source_name: MEF cell line

label_protocol: cRNA was generated according to the Affymetrix protocol.

extract_protocol: Total RNA was extracted and purified from cell lines using the Quiagen RNeasy Mini Kit (Qiagen, Valencia, CA) as suggested by the manufacturer. RNAs were then quantified and inspected by Bioanalyzer (Agilent Technologies) analysis.


title: Chimpanzee cerebellum, biological rep 3

organism: Pan troglodytes

source_name: chimpanzee cerebellum

value: 30 years